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- PDB-4s15: Crystal structure of the orphan nuclear receptor RORalpha ligand-... -

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Basic information

Entry
Database: PDB / ID: 4s15
TitleCrystal structure of the orphan nuclear receptor RORalpha ligand-binding domain in complex with 4alpha-caboxyl, 4beta-methyl-zymosterol (4ACD8)
Components
  • Nuclear receptor ROR-alpha
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


ovarian follicle rupture / cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity ...ovarian follicle rupture / cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of circadian rhythm / lipid storage / oxysterol binding / regulation of smoothened signaling pathway / muscle cell differentiation / triglyceride homeostasis / regulation of macrophage activation / negative regulation of fat cell differentiation / histone deacetylase complex / regulation of glucose metabolic process / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / nuclear retinoid X receptor binding / intracellular receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / : / nitric oxide biosynthetic process / xenobiotic metabolic process / SUMOylation of transcription cofactors / cholesterol homeostasis / transcription coregulator binding / transcription corepressor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / Heme signaling / transcription coactivator binding / PPARA activates gene expression / beta-catenin binding / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / histone deacetylase binding / fibrillar center / nuclear receptor activity / circadian rhythm / transcription corepressor activity / : / cellular response to tumor necrosis factor / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to hypoxia / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Nuclear receptor ROR ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4D8 / Nuclear receptor ROR-alpha / Nuclear receptor-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsHuang, P. / Santori, F.R. / Littman, D.R. / Rastinejad, F.
CitationJournal: Cell Metab / Year: 2015
Title: Identification of Natural ROR gamma Ligands that Regulate the Development of Lymphoid Cells.
Authors: Santori, F.R. / Huang, P. / van de Pavert, S.A. / Douglass, E.F. / Leaver, D.J. / Haubrich, B.A. / Keber, R. / Lorbek, G. / Konijn, T. / Rosales, B.N. / Rozman, D. / Horvat, S. / Rahier, A. ...Authors: Santori, F.R. / Huang, P. / van de Pavert, S.A. / Douglass, E.F. / Leaver, D.J. / Haubrich, B.A. / Keber, R. / Lorbek, G. / Konijn, T. / Rosales, B.N. / Rozman, D. / Horvat, S. / Rahier, A. / Mebius, R.E. / Rastinejad, F. / Nes, W.D. / Littman, D.R.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-alpha
C: Nuclear receptor-interacting protein 1
B: Nuclear receptor ROR-alpha
D: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5228
Polymers62,4524
Non-polymers1,0704
Water5,585310
1
A: Nuclear receptor ROR-alpha
C: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7614
Polymers31,2262
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-6 kcal/mol
Surface area11990 Å2
MethodPISA
2
B: Nuclear receptor ROR-alpha
D: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7614
Polymers31,2262
Non-polymers5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.194, 80.305, 113.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor ROR-alpha / Nuclear receptor RZR-alpha / Nuclear receptor subfamily 1 group F member 1 / RAR-related orphan ...Nuclear receptor RZR-alpha / Nuclear receptor subfamily 1 group F member 1 / RAR-related orphan receptor A / Retinoid-related orphan receptor-alpha


Mass: 29845.504 Da / Num. of mol.: 2 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1F1, RORA, RZRA / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P35398
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 1380.632 Da / Num. of mol.: 2 / Fragment: LxxLL binding motif / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P48552
#3: Chemical ChemComp-4D8 / (3beta,4alpha,5beta,14beta)-3-hydroxy-4-methylcholesta-8,24-diene-4-carboxylic acid / 4alpha-carboxy-4beta-methyl-zymosterol


Mass: 442.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H46O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM MgCl2, 9%-21% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.897→50 Å / Num. all: 52067 / Num. obs: 51703 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.108 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.897→46.237 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2641 5.12 %RANDOM
Rwork0.1739 ---
all0.176 52049 --
obs0.176 51607 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.897→46.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 76 310 4581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054417
X-RAY DIFFRACTIONf_angle_d0.9075982
X-RAY DIFFRACTIONf_dihedral_angle_d14.8911697
X-RAY DIFFRACTIONf_chiral_restr0.037678
X-RAY DIFFRACTIONf_plane_restr0.003750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8972-1.93170.29081360.25352427X-RAY DIFFRACTION95
1.9317-1.96890.24811550.22132519X-RAY DIFFRACTION99
1.9689-2.00910.23651390.20542535X-RAY DIFFRACTION99
2.0091-2.05270.27861410.20052556X-RAY DIFFRACTION100
2.0527-2.10050.23721310.19142577X-RAY DIFFRACTION100
2.1005-2.1530.20291580.17472549X-RAY DIFFRACTION100
2.153-2.21120.21521410.1692553X-RAY DIFFRACTION100
2.2112-2.27630.18391190.1632600X-RAY DIFFRACTION100
2.2763-2.34980.20891140.16862606X-RAY DIFFRACTION100
2.3498-2.43370.22181430.17082587X-RAY DIFFRACTION100
2.4337-2.53120.23221360.17472558X-RAY DIFFRACTION100
2.5312-2.64640.231490.18042588X-RAY DIFFRACTION100
2.6464-2.78590.24851320.18892611X-RAY DIFFRACTION100
2.7859-2.96040.21371500.18642591X-RAY DIFFRACTION100
2.9604-3.18890.27171280.18852594X-RAY DIFFRACTION100
3.1889-3.50970.19831470.17062597X-RAY DIFFRACTION100
3.5097-4.01730.17821390.15222620X-RAY DIFFRACTION99
4.0173-5.06040.16781340.14372623X-RAY DIFFRACTION98
5.0604-46.25120.21951490.18012675X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0896-0.137-2.43222.6918-0.34095.20030.17130.42550.1359-0.51150.002-0.17620.0067-0.09340.01460.2720.03870.07530.23180.00120.205618.259425.6592-4.9829
25.92990.526-0.96891.87250.22511.5952-0.06190.2575-0.4982-0.2011-0.1612-0.15680.01160.09430.16050.1879-0.0007-0.04630.2347-0.02030.2575-4.930221.04673.4791
32.6428-0.6833-1.41690.87990.87611.6952-0.0986-0.0728-0.16950.0588-0.02320.16680.0835-0.04720.05710.15350.00680.00060.11010.02160.1417-2.020629.209417.2084
43.07570.6332-0.33331.66170.1811.09680.03560.05670.0678-0.1644-0.0185-0.0563-0.14180.0772-0.0070.1954-0.00350.01610.15840.00530.12636.631131.7867.2711
52.8765-1.1733-1.8052.02530.9554.44580.20620.44110.087-0.1456-0.17010.1215-0.3212-0.1555-0.0510.18950.0356-0.0170.20090.00650.1989-7.079238.04837.6676
64.29710.47530.31553.90330.81863.86520.2776-0.04330.40340.0021-0.3895-0.1317-0.44280.0515-0.02160.2821-0.00760.05460.20450.05880.192513.987936.74681.8097
75.95311.14662.50783.29951.06325.89820.00620.4376-0.0307-0.6340.0023-0.1613-0.4473-0.0085-0.06110.37420.05660.09610.26220.06410.213316.331836.2552-8.0432
81.0287-0.4311-0.86891.30720.17582.60090.16920.07570.1533-0.17170.0377-0.163-0.23170.1093-0.110.2213-0.00420.02160.1592-0.00310.22554.868540.242915.1717
92.08571.8395-1.05962.0048-1.72432.43750.24250.1270.45280.31-0.1628-0.3505-0.33540.5557-0.02460.232-0.0226-0.01860.19380.03050.227620.639429.273319.1048
105.8387-2.7650.13275.30921.39241.9816-0.06560.23040.2562-0.9267-0.1753-1.20850.26531.1439-0.16890.28740.09150.1990.62950.11220.505634.568114.578526.1648
111.9613-0.6762-0.81914.58814.48425.73690.4570.02870.4965-0.40780.4985-1.3332-0.48090.30330.20780.3497-0.08850.01620.3627-0.10320.353424.216129.169736.6293
122.7757-0.17440.44661.49770.23561.2071-0.151-0.23210.23640.0812-0.01510.0924-0.19850.00880.06770.2023-0.014-0.03310.13180.00590.15718.535727.187135.9634
132.39870.78060.76654.44581.18983.93170.0490.1422-0.1477-0.3422-0.0026-0.31830.01050.11540.03760.18440.02560.03280.16850.01840.202818.324911.967425.7752
143.113-0.74580.41442.4638-0.2442.4095-0.0647-0.1569-0.04540.4118-0.0047-0.1406-0.10340.12230.06550.2899-0.0044-0.0420.2082-0.0090.159412.336121.66245.1663
154.04872.09461.42533.5111.29143.1478-0.08570.1119-0.1474-0.07410.1376-0.26190.01380.44570.00420.15890.02940.02270.25880.03890.221922.63528.300330.4378
164.73060.83211.51984.57431.15845.30380.2623-0.116-0.5460.54180.1574-1.24760.47390.9167-0.06120.23880.0859-0.02590.41810.04530.524632.13715.293733.2766
176.0053-1.52080.90282.8285-0.92281.29940.1561-0.2769-0.23880.0147-0.112-0.10210.10730.08570.04280.1886-0.01440.01580.16570.02450.232910.4859.525637.6304
181.9675-1.2289-0.45823.83540.21471.26710.06190.1003-0.1516-0.3335-0.13550.2492-0.0579-0.02130.07670.2315-0.0009-0.04650.20760.00270.18070.572415.591723.8848
197.2072-1.86130.1112.074-0.81086.43330.04020.1711-0.1222-0.1275-0.3754-0.13020.66260.38750.3920.33420.02690.04990.22970.04340.213312.520515.964214.1289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 287 )
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 340 )
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 387 )
5X-RAY DIFFRACTION5chain 'A' and (resid 388 through 413 )
6X-RAY DIFFRACTION6chain 'A' and (resid 414 through 438 )
7X-RAY DIFFRACTION7chain 'A' and (resid 439 through 463 )
8X-RAY DIFFRACTION8chain 'A' and (resid 464 through 512 )
9X-RAY DIFFRACTION9chain 'C' and (resid 498 through 506 )
10X-RAY DIFFRACTION10chain 'B' and (resid 269 through 287 )
11X-RAY DIFFRACTION11chain 'B' and (resid 288 through 298 )
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 340 )
13X-RAY DIFFRACTION13chain 'B' and (resid 341 through 371 )
14X-RAY DIFFRACTION14chain 'B' and (resid 372 through 413 )
15X-RAY DIFFRACTION15chain 'B' and (resid 414 through 438 )
16X-RAY DIFFRACTION16chain 'B' and (resid 439 through 465 )
17X-RAY DIFFRACTION17chain 'B' and (resid 466 through 494 )
18X-RAY DIFFRACTION18chain 'B' and (resid 495 through 518 )
19X-RAY DIFFRACTION19chain 'D' and (resid 498 through 506 )

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